data_preparacion

R/data_building.R

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+
+#' @keywords internal
+# perutimber_especies list ------------------------------------------------
+#' lista de especies presentes en la base de datos perutimber
+#' se debe conciderar que las combinaciones de input_genus, input_epitheton,
+#' input_subspecies_epitheton son unicos,
+#' los valores de  accepted_name pueden repetirse
+#'
+#' pt_df <- readxl::read_xlsx("tab_perutimber.xlsx") |>
+#'   dplyr::mutate(scientific_name = paste0(input_genus, " ",
+#'                                          input_epitheton)) |>
+#'   dplyr::mutate(scientific_name = dplyr::case_when(
+#'     rank == "subspecies" ~ paste0(input_genus, " ",
+#'                                   input_epitheton, " ",
+#'                                   "subsp. ",
+#'                                   input_subspecies_epitheton),
+#'     rank == "variety" ~ paste0(input_genus, " ",
+#'                                input_epitheton, " ",
+#'                                "var. ",
+#'                                input_subspecies_epitheton),
+#'     TRUE ~ scientific_name
+#'   )) |>
+#'   dplyr::mutate(scientific_name = dplyr::case_when(
+#'     !is.na(accepted_name_author) ~ paste0(scientific_name, " ",
+#'                                           accepted_name_author),
+#'     TRUE ~ scientific_name
+#'   )) |>
+#'   dplyr::arrange(accepted_family, input_genus) |>
+#'   dplyr::mutate(id_cat = paste0( dplyr::row_number(),
+#'                                  stringr::str_sub(input_genus, 1, 2),
+#'                                  stringr::str_sub(input_epitheton, 1, 2)) |>
+#'                   toupper())
+#' pt_df
+#' # revisa que los nombres completos sean unicos
+#'
+#' pt_df |>
+#'   dplyr::add_count(scientific_name) |>
+#'   dplyr::filter(n > 1)
+#'
+#' # TAB_PERUTIMBER ----------------------------------------------------------
+#' #' esta base de datos debe ser guardada en una base de datos de tipo
+#' #' data.frame
+#' names_tab_perutimber <- c("id_cat", "input_genus", "input_epitheton",
+#'                           "rank", "input_subspecies_epitheton", "taxonomic_status",
+#'                           "accepted_name", "accepted_family", "accepted_name_author",
+#'                           "tnrs_name_id", "accepted_name_url", "source")
+#' names_tab_perutimber |> length()
+#'
+#' tab_perutimber <- pt_df |>
+#'   dplyr::select( dplyr::all_of(names_tab_perutimber)) |>
+#'   as.data.frame()
+#' tab_perutimber
+#'
+#' # PERUTIMBER SPS CLASS ----------------------------------------------------
+#' #' esta debe almacenarce como matrx o array
+#' names_sps_class <- c("species", "genus", "epithet", "author",
+#'                      "subspecies", "variety",
+#'                      "subvariety", "forma", "subforma", "id")
+#'
+#' perutimber_sps_class <- pt_df |>
+#'   dplyr::select(species = scientific_name,
+#'                 genus = input_genus,
+#'                 epithet = input_epitheton,
+#'                 author = accepted_name_author,
+#'                 input_subspecies_epitheton,
+#'                 rank) |>
+#'   dplyr::mutate(subspecies =  dplyr::case_when(
+#'     rank == "subspecies" ~ input_subspecies_epitheton,
+#'     TRUE ~ ""
+#'   ),
+#'   variety =  dplyr::case_when(
+#'     rank == "variety" ~ input_subspecies_epitheton,
+#'     TRUE ~ ""
+#'   ),
+#'   subvariety = "",
+#'   forma = "",
+#'   subforma = "",
+#'   id =  dplyr::row_number()) |>
+#'   dplyr::select( dplyr::all_of(names_sps_class)) |>
+#'   dplyr::mutate_all(~as.character(.) |>
+#'                       toupper()) |>
+#'   as.matrix.data.frame()
+#'
+#' perutimber_sps_class |>
+#'   class()
+#'
+#' # TAB POSSITION -----------------------------------------------------------
+#' #' esta debe ser guardada como data.frame
+#' #' perutimber::tab_perutimber_position
+#' names_posistion = c("position", "triphthong", "genus")
+#'
+#' tab_perutimber_position <- pt_df |>
+#'   dplyr::select(genus = input_genus) |>
+#'   dplyr::mutate(id =  dplyr::row_number(),
+#'                 triphthong = stringr::str_sub(genus, 1, 3)) |>
+#'   dplyr::mutate_if(is.character, ~toupper(.)) |>
+#'   dplyr::group_by(genus, triphthong) |>
+#'   dplyr::summarise(position = min(id),
+#'                    .groups = "drop") |>
+#'   dplyr::arrange(position) |>
+#'   as.data.frame()
+#'
+#' tab_perutimber_position
+#'
+#' # save clean data ---------------------------------------------------------
+#' tab_perutimber |>
+#'   save(file = "data/tab_perutimber.rda")
+#' perutimber_sps_class |>
+#'   save(file = "data/perutimber_sps_class.rda")
+#' tab_perutimber_position |>
+#'   save(file = "data/tab_perutimber_position.rda")
+#'